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Items: 1 to 50 of 299

1.

SPar-K : a method to partition NGS signal data.

Groux R, Bucher P.

Bioinformatics. 2019 May 22. pii: btz416. doi: 10.1093/bioinformatics/btz416. [Epub ahead of print]

PMID:
31116370
2.

Chromatin three-dimensional interactions mediate genetic effects on gene expression.

Delaneau O, Zazhytska M, Borel C, Giannuzzi G, Rey G, Howald C, Kumar S, Ongen H, Popadin K, Marbach D, Ambrosini G, Bielser D, Hacker D, Romano L, Ribaux P, Wiederkehr M, Falconnet E, Bucher P, Bergmann S, Antonarakis SE, Reymond A, Dermitzakis ET.

Science. 2019 May 3;364(6439). pii: eaat8266. doi: 10.1126/science.aat8266.

PMID:
31048460
3.

Short-lived AUF1 p42-binding mRNAs of RANKL and BCL6 have two distinct instability elements each.

Dogar AM, Pauchard-Batschulat R, Grisoni-Neupert B, Richman L, Paillusson A, Pradervand S, Hagenbüchle O, Ambrosini G, Schmid CD, Bucher P, Kühn LC.

PLoS One. 2018 Nov 12;13(11):e0206823. doi: 10.1371/journal.pone.0206823. eCollection 2018.

4.

Detection and benchmarking of somatic mutations in cancer genomes using RNA-seq data.

Coudray A, Battenhouse AM, Bucher P, Iyer VR.

PeerJ. 2018 Jul 31;6:e5362. doi: 10.7717/peerj.5362. eCollection 2018.

5.

A fluorescence anisotropy assay to discover and characterize ligands targeting the maytansine site of tubulin.

Menchon G, Prota AE, Lucena-Agell D, Bucher P, Jansen R, Irschik H, Müller R, Paterson I, Díaz JF, Altmann KH, Steinmetz MO.

Nat Commun. 2018 May 29;9(1):2106. doi: 10.1038/s41467-018-04535-8.

6.

NF-κB Activation in Lymphoid Malignancies: Genetics, Signaling, and Targeted Therapy.

Grondona P, Bucher P, Schulze-Osthoff K, Hailfinger S, Schmitt A.

Biomedicines. 2018 Mar 26;6(2). pii: E38. doi: 10.3390/biomedicines6020038. Review.

7.

PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix.

Ambrosini G, Groux R, Bucher P.

Bioinformatics. 2018 Jul 15;34(14):2483-2484. doi: 10.1093/bioinformatics/bty127.

8.

MGA repository: a curated data resource for ChIP-seq and other genome annotated data.

Dréos R, Ambrosini G, Groux R, Périer RC, Bucher P.

Nucleic Acids Res. 2018 Jan 4;46(D1):D175-D180. doi: 10.1093/nar/gkx995.

9.

SMiLE-seq identifies binding motifs of single and dimeric transcription factors.

Isakova A, Groux R, Imbeault M, Rainer P, Alpern D, Dainese R, Ambrosini G, Trono D, Bucher P, Deplancke B.

Nat Methods. 2017 Mar;14(3):316-322. doi: 10.1038/nmeth.4143. Epub 2017 Jan 16.

PMID:
28092692
10.

The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms.

Dreos R, Ambrosini G, Groux R, Cavin Périer R, Bucher P.

Nucleic Acids Res. 2017 Jan 4;45(D1):D51-D55. doi: 10.1093/nar/gkw1069. Epub 2016 Nov 28.

11.

SNP2TFBS - a database of regulatory SNPs affecting predicted transcription factor binding site affinity.

Kumar S, Ambrosini G, Bucher P.

Nucleic Acids Res. 2017 Jan 4;45(D1):D139-D144. doi: 10.1093/nar/gkw1064. Epub 2016 Nov 28.

12.

The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data.

Ambrosini G, Dreos R, Kumar S, Bucher P.

BMC Genomics. 2016 Nov 18;17(1):938.

13.

Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters.

Dreos R, Ambrosini G, Bucher P.

PLoS Comput Biol. 2016 Oct 7;12(10):e1005144. doi: 10.1371/journal.pcbi.1005144. eCollection 2016 Oct.

14.

Similar and Different? Subjective Effects of Methylphenidate and Cocaine in Opioid-Maintained Patients.

Vogel M, Bucher P, Strasser J, Liechti ME, Krähenbühl S, Dürsteler KM.

J Psychoactive Drugs. 2016 Apr-Jun;48(2):93-100. doi: 10.1080/02791072.2015.1130883. Epub 2016 Mar 3.

PMID:
26940988
15.

A maximum-likelihood approach for building cell-type trees by lifting.

Nair NU, Hunter L, Shao M, Grnarova P, Lin Y, Bucher P, E Moret BM.

BMC Genomics. 2016 Jan 11;17 Suppl 1:14. doi: 10.1186/s12864-015-2297-3.

16.

Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features.

Kumar S, Bucher P.

BMC Bioinformatics. 2016 Jan 11;17 Suppl 1:4. doi: 10.1186/s12859-015-0846-z.

17.

Total Synthesis and Biological Assessment of Mandelalide A.

Brütsch TM, Bucher P, Altmann KH.

Chemistry. 2016 Jan 22;22(4):1292-300. doi: 10.1002/chem.201504230. Epub 2015 Dec 7.

PMID:
26639765
18.

Incarcerated Grynfeltt-Lesshaft Hernia.

Scheffler M, Renard J, Bucher P, Botsikas D.

J Radiol Case Rep. 2015 Apr 30;9(4):9-13. doi: 10.3941/jrcr.v9i4.2073. eCollection 2015 Apr.

19.

The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools.

Dreos R, Ambrosini G, Périer RC, Bucher P.

Nucleic Acids Res. 2015 Jan;43(Database issue):D92-6. doi: 10.1093/nar/gku1111. Epub 2014 Nov 6.

20.

Chemically induced mouse liver tumors are resistant to treatment with atorvastatin.

Braeuning A, Bucher P, Hofmann U, Buchmann A, Schwarz M.

BMC Cancer. 2014 Oct 15;14:766. doi: 10.1186/1471-2407-14-766.

21.

Study of cell differentiation by phylogenetic analysis using histone modification data.

Nair NU, Lin Y, Manasovska A, Antic J, Grnarova P, Sahu AD, Bucher P, Moret BM.

BMC Bioinformatics. 2014 Aug 8;15:269. doi: 10.1186/1471-2105-15-269.

22.

Classification of selectively constrained DNA elements using feature vectors and rule-based classifiers.

Polychronopoulos D, Weitschek E, Dimitrieva S, Bucher P, Felici G, Almirantis Y.

Genomics. 2014 Aug;104(2):79-86. doi: 10.1016/j.ygeno.2014.07.004. Epub 2014 Jul 22.

23.

Probabilistic partitioning methods to find significant patterns in ChIP-Seq data.

Nair NU, Kumar S, Moret BM, Bucher P.

Bioinformatics. 2014 Sep 1;30(17):2406-13. doi: 10.1093/bioinformatics/btu318. Epub 2014 May 7.

PMID:
24812341
24.

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support.

Stockinger H, Altenhoff AM, Arnold K, Bairoch A, Bastian F, Bergmann S, Bougueleret L, Bucher P, Delorenzi M, Lane L, Le Mercier P, Lisacek F, Michielin O, Palagi PM, Rougemont J, Schwede T, von Mering C, van Nimwegen E, Walther D, Xenarios I, Zavolan M, Zdobnov EM, Zoete V, Appel RD.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W436-41. doi: 10.1093/nar/gku380. Epub 2014 May 3.

25.

Prefabricated fibular flaps for reconstruction of defects of the maxillofacial skeleton: planning, technique, and long-term experience.

Rohner D, Bucher P, Hammer B.

Int J Oral Maxillofac Implants. 2013 Sep-Oct;28(5):e221-9. doi: 10.11607/jomi.te01.

PMID:
24066339
26.

Nuclear Factor I genomic binding associates with chromatin boundaries.

Pjanic M, Schmid CD, Gaussin A, Ambrosini G, Adamcik J, Pjanic P, Plasari G, Kerschgens J, Dietler G, Bucher P, Mermod N.

BMC Genomics. 2013 Feb 12;14:99. doi: 10.1186/1471-2164-14-99.

27.

Importance of patient-specific intraoperative guides in complex maxillofacial reconstruction.

Rohner D, Guijarro-Martínez R, Bucher P, Hammer B.

J Craniomaxillofac Surg. 2013 Jul;41(5):382-90. doi: 10.1016/j.jcms.2012.10.021. Epub 2012 Dec 8.

PMID:
23228282
28.

Transarterial embolization in acute colonic bleeding: review of 11 years of experience and long-term results.

Rossetti A, Buchs NC, Breguet R, Bucher P, Terraz S, Morel P.

Int J Colorectal Dis. 2013 Jun;28(6):777-82. doi: 10.1007/s00384-012-1621-5. Epub 2012 Dec 4.

PMID:
23208010
29.

EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era.

Dreos R, Ambrosini G, Cavin Périer R, Bucher P.

Nucleic Acids Res. 2013 Jan;41(Database issue):D157-64. doi: 10.1093/nar/gks1233. Epub 2012 Nov 27.

30.

UCNEbase--a database of ultraconserved non-coding elements and genomic regulatory blocks.

Dimitrieva S, Bucher P.

Nucleic Acids Res. 2013 Jan;41(Database issue):D101-9. doi: 10.1093/nar/gks1092. Epub 2012 Nov 27.

31.

Images in emergency medicine. Elderly male with respiratory failure. Chronic idiopathic intestinal pseudo-obstruction.

Rigamonti F, Bucher P, Nguyen-Tang T, Merlani P.

Ann Emerg Med. 2012 Oct;60(4):423, 430. doi: 10.1016/j.annemergmed.2012.04.026. No abstract available.

PMID:
23010179
32.

Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements.

Dimitrieva S, Bucher P.

Bioinformatics. 2012 Sep 15;28(18):i395-i401. doi: 10.1093/bioinformatics/bts400.

33.

Robotic single-incision laparoscopic cholecystectomy.

Morel P, Pugin F, Bucher P, Buchs NC, Hagen ME.

J Robot Surg. 2012 Sep;6(3):273-4. doi: 10.1007/s11701-011-0310-7. Epub 2011 Oct 22. No abstract available.

34.

ChIPnorm: a statistical method for normalizing and identifying differential regions in histone modification ChIP-seq libraries.

Nair NU, Sahu AD, Bucher P, Moret BM.

PLoS One. 2012;7(8):e39573. doi: 10.1371/journal.pone.0039573. Epub 2012 Aug 3.

35.

[Personal factors of the ICF].

Grotkamp S, Cibis W, Nüchtern E, Baldus A, Behrens J, Bucher PO, Dommen Nyffeler I, Gmünder HP, Gutenbrunner C, Hagen T, Keller K, Pöthig D, Queri S, Rentsch HP, Rink M, Schian H, Schian M, Schwarze M, von Mittelstaedt G, Seger W.

Gesundheitswesen. 2012 Jul;74(7):449-58. doi: 10.1055/s-0032-1314823. Epub 2012 Jul 17. German.

PMID:
22814994
36.

Practicality and time complexity of a sparsified RNA folding algorithm.

Dimitrieva S, Bucher P.

J Bioinform Comput Biol. 2012 Apr;10(2):1241007. doi: 10.1142/S0219720012410077.

PMID:
22809342
37.

Intra-operative fluorescent cholangiography using indocyanin green during robotic single site cholecystectomy.

Buchs NC, Hagen ME, Pugin F, Volonte F, Bucher P, Schiffer E, Morel P.

Int J Med Robot. 2012 Dec;8(4):436-40. doi: 10.1002/rcs.1437. Epub 2012 May 31.

PMID:
22648637
38.

Cholecystectomy through single access endoscopic surgery: where do we stand?

Bucher P.

Minerva Chir. 2012 Apr;67(2):97-104. Review.

PMID:
22487912
39.

Value of performing routine postoperative liquid contrast swallow studies following robot-assisted Roux-en-Y gastric bypass.

Buchs NC, Bucher P, Pugin F, Hagen ME, Chassot G, Koutny-Fong P, Morel P.

Swiss Med Wkly. 2012 Apr 5;142:w13556. doi: 10.4414/smw.2012.13556. eCollection 2012.

40.

Robotic pancreatic resection: how far can we go?

Buchs NC, Volonte F, Pugin F, Bucher P, Jung M, Morel P.

Minerva Chir. 2011 Dec;66(6):603-14. Review.

PMID:
22233666
41.

RNA profiling and chromatin immunoprecipitation-sequencing reveal that PTF1a stabilizes pancreas progenitor identity via the control of MNX1/HLXB9 and a network of other transcription factors.

Thompson N, Gésina E, Scheinert P, Bucher P, Grapin-Botton A.

Mol Cell Biol. 2012 Mar;32(6):1189-99. doi: 10.1128/MCB.06318-11. Epub 2012 Jan 9.

42.

An evaluation of face-bow transfer for the planning of orthognathic surgery.

Zizelmann C, Hammer B, Gellrich NC, Schwestka-Polly R, Rana M, Bucher P.

J Oral Maxillofac Surg. 2012 Aug;70(8):1944-50. doi: 10.1016/j.joms.2011.08.025. Epub 2011 Nov 12.

PMID:
22079061
43.

Learning curve for robot-assisted Roux-en-Y gastric bypass.

Buchs NC, Pugin F, Bucher P, Hagen ME, Chassot G, Koutny-Fong P, Morel P.

Surg Endosc. 2012 Apr;26(4):1116-21. doi: 10.1007/s00464-011-2008-3. Epub 2011 Nov 2.

PMID:
22044973
44.

History of robotic surgery: from AESOP® and ZEUS® to da Vinci®.

Pugin F, Bucher P, Morel P.

J Visc Surg. 2011 Oct;148(5 Suppl):e3-8. doi: 10.1016/j.jviscsurg.2011.04.007. Epub 2011 Oct 4. Review. No abstract available.

PMID:
21974854
45.

Randomized clinical trial of laparoendoscopic single-site versus conventional laparoscopic cholecystectomy.

Bucher P, Pugin F, Buchs NC, Ostermann S, Morel P.

Br J Surg. 2011 Dec;98(12):1695-702. doi: 10.1002/bjs.7689. Epub 2011 Sep 30.

PMID:
21964736
46.

Robotic single-port cholecystectomy using a new platform: initial clinical experience.

Morel P, Hagen ME, Bucher P, Buchs NC, Pugin F.

J Gastrointest Surg. 2011 Dec;15(12):2182-6. doi: 10.1007/s11605-011-1688-2. Epub 2011 Sep 27.

PMID:
21948180
47.

A gene-rich, transcriptionally active environment and the pre-deposition of repressive marks are predictive of susceptibility to KRAB/KAP1-mediated silencing.

Meylan S, Groner AC, Ambrosini G, Malani N, Quenneville S, Zangger N, Kapopoulou A, Kauzlaric A, Rougemont J, Ciuffi A, Bushman FD, Bucher P, Trono D.

BMC Genomics. 2011 Jul 26;12:378. doi: 10.1186/1471-2164-12-378.

48.

Totally robotic right colectomy: a preliminary case series and an overview of the literature.

Buchs NC, Pugin F, Bucher P, Morel P.

Int J Med Robot. 2011 Sep;7(3):348-52. doi: 10.1002/rcs.404. Epub 2011 Jun 15. Review.

PMID:
21678543
49.

BlastR--fast and accurate database searches for non-coding RNAs.

Bussotti G, Raineri E, Erb I, Zytnicki M, Wilm A, Beaudoing E, Bucher P, Notredame C.

Nucleic Acids Res. 2011 Sep 1;39(16):6886-95. doi: 10.1093/nar/gkr335. Epub 2011 May 30.

50.

ZFN-site searches genomes for zinc finger nuclease target sites and off-target sites.

Cradick TJ, Ambrosini G, Iseli C, Bucher P, McCaffrey AP.

BMC Bioinformatics. 2011 May 13;12:152. doi: 10.1186/1471-2105-12-152.

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